title: New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance.
abstract: Mycobacterium abscessus (M. abscessus sensu lato, or the M. abscessus group) comprises three closely related taxa whose taxonomic statuses are under revision, i.e., M. abscessus sensu stricto, Mycobacterium bolletii, and Mycobacterium massiliense. We describe here a simple, robust, and cost-effective PCR-based method for distinguishing among M. abscessus, M. massiliense, and M. bolletii. Based on the M. abscessus ATCC 19977(T) genome, regions that discriminated between M. abscessus and M. massiliense were identified through array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense, and 2 M. bolletii isolates previously identified by multitarget sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full-length erm(41) gene instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for straightforward identification of M. abscessus, M. massiliense, and M. bolletii and the assessment of inducible clarithromycin resistance. This method can be easily integrated into a routine workflow to provide subspecies-level identification within 24 h after isolation of the M. abscessus group.
authors.affiliation: Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: Shamira J
authors.initials: SJ
authors.lastname: Shallom
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Gardina
authors.forename: Timothy G
authors.initials: TG
authors.lastname: Myers
authors.forename: Yinong
authors.initials: Y
authors.lastname: Sebastian
authors.forename: Patricia
authors.initials: P
authors.lastname: Conville
authors.forename: Leslie B
authors.initials: LB
authors.lastname: Calhoun
authors.forename: Hervé
authors.initials: H
authors.lastname: Tettelin
authors.forename: Kenneth N
authors.initials: KN
authors.lastname: Olivier
authors.forename: Gulbu
authors.initials: G
authors.lastname: Uzel
authors.forename: Elizabeth P
authors.initials: EP
authors.lastname: Sampaio
authors.forename: Steven M
authors.initials: SM
authors.lastname: Holland
authors.forename: Adrian M
authors.initials: AM
authors.lastname: Zelazny
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D001431:Bacteriological Techniques / Q000379:methods*; D017291:Clarithromycin / Q000494:pharmacology*; D055028:Comparative Genomic Hybridization; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024881:Drug Resistance, Bacterial; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D014644:Genetic Variation; D006801:Humans; D008969:Molecular Sequence Data; D009170:Nontuberculous Mycobacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D000900:Anti-Bacterial Agents; D017931:DNA Primers; D004269:DNA, Bacterial; D017291:Clarithromycin